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GENOME ANALYSIS

Identification and Characterization of Lineage-Specific Genes within the Poaceae^1,[W],[OA]

The Institute for Genomic Research and J. Craig Venter Institute, Rockville, Maryland 20850 (M.A.C., W.Z., H.L., S.O., K.L.C., B.J.H., J.P.H., C.R.B.); and Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 (N.J.)

Using the rice (Oryza sativa) sp. japonica genome annotation, along with genomic sequence and clustered transcript assemblies from 184 species in the plant kingdom, we have identified a set of 861 rice genes that are evolutionarily conserved among six diverse species within the Poaceae yet lack significant sequence similarity with plant species outside the Poaceae. This set of evolutionarily conserved and lineage-specific rice genes is termed conserved Poaceae-specific genes (CPSGs) to reflect the presence of significant sequence similarity across three separate Poaceae subfamilies. The vast majority of rice CPSGs (86.6%) encode proteins with no putative function or functionally characterized protein domain. For the remaining CPSGs, 8.8% encode an F-box domain-containing protein and 4.5% encode a protein with a putative function. On average, the CPSGs have fewer exons, shorter total gene length, and elevated GC content when compared with genes annotated as either transposable elements (TEs) or those genes having significant sequence similarity in a species outside the Poaceae. Multiple sequence alignments of the CPSGs with sequences from other Poaceae species show conservation across a putative domain, a novel domain, or the entire coding length of the protein. At the genome level, syntenic alignments between sorghum (Sorghum bicolor) and 103 of the 861 rice CPSGs (12.0%) could be made, demonstrating an additional level of conservation for this set of genes within the Poaceae. The extensive sequence similarity in evolutionarily distinct species within the Poaceae family and an additional screen for TE-related structural characteristics and sequence discounts these CPSGs as being misannotated TEs. Collectively, these data confirm that we have identified a specific set of genes that are highly conserved within, as well as specific to, the Poaceae.

² Present address: Pioneer Hi-Bred International, 7300 NW 62nd Ave., Johnston, IA 50131.

³ Present address: Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824.

⁴ Present address: The Broad Institute, 7 Cambridge Center, Cambridge, MA 02142.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: C. Robin Buell (buell{at}msu.edu).

^[W] The online version of this article contains Web-only data.

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.107.104513

^* Corresponding author; e-mail buell{at}msu.edu.

Received June 25, 2007; accepted October 14, 2007; published October 19, 2007.

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